


Chuck VS The Last Ship

by Ambear9



Series: Chuck vs. Short Stories [11]
Category: Chuck (TV), The Last Ship (TV)
Genre: Character Death, John Casey is Mike Slattery, M/M, Mash Up, wow i wrote something without sex lol
Language: English
Status: Completed
Published: 2019-03-28
Updated: 2019-03-28
Packaged: 2019-12-26 01:01:25
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 1
Words: 3,491
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/18272603
Author URL: https://archiveofourown.org/users/Ambear9/pseuds/Ambear9
Summary: When the show ended Sarah left Chuck sitting on the beach alone and he never saw her again. Chuck and Morgan kept Carmichael Industries running by helping the CIA with cyber terrorism.After a few months Gertrude broke Casey's heart so he took a few months off before calling The General and asking to come back to the CIA, he was sent undercover on a Navy ship called the Nathan James where he would be Executive Officer Mike Slattery. It was two years in when fate brought Chuck aboard to check on their computer system that had been hacked, then all hell breaks loose.





	Chuck VS The Last Ship

**Author's Note:**

> When I first watched The Last Ship I imagined that Casey was sent undercover on a mission aboard the Nathan James as XO Mike Slattery. So I decided to write about it. Loosely based on events from the show, don't need to have any knowledge of it to read this fic but there are a few tiny spoilers.

Chuck had been on many helicopters but this was the first time he has ever been on one that was landing on a Navy ship in the middle of the ocean, to say he was scared was an understatement.  
When he got out of the helicopter he was met by the Captain of the ship  
“Hello, you must be Charles Carmichael, I'm Captain Tom Chandler” he shook Chuck's hand.  
“Yeah, but you can call me Chuck”  
“Okay Chuck, I'll take you inside to Lieutenant Kara Foster, she will show you around the ship, get you set up in your bunk then take you down to the computers. When you are done I'd like you to come up to the bridge and fill me in”  
“Sounds good” thankfully Chuck researched stuff about Navy ships before he came out and knew what that meant.

 

After a very confusing tour and a quick check of the computers Kara lead Chuck up to the bridge, Chandler turned his chair “Please tell me everything is good”  
The guy in the chair next to Chandler turned his chair around to join the conversation and Chuck almost passed out. “Mike this is Chuck, the computer guy they flew in”  
Mike nodded at him “Bartowski?”  
"What the hell is a Bartowski?" Chandler asked.  
“Oh my god you're alive” Chuck had to hold himself up.  
“Kara did he hit his head while he was down there?” The Captain raised a brow  
“No Sir, I'm not sure what is going on”  
“Tom I need a minute with him, I'll explain later”  
Chandler nodded as Mike grabbed Chuck's arm leading him down to his room.  
“Casey you, how is this, I can't believe, oh my god”  
“You can't call me that, I'm not John Casey on this ship I'm Mike Slattery”  
“First of all that is a way cooler name, secondly I have a million questions but I'll start with wow you’re eyes look even more amazing when you wear blue and first question is why do you have a framed picture of a girl and two kids next to your bed?”  
Casey played with the ring on his finger “They are my cover wife Christine and my two kids, Hannah and Lucas, and fun fact I used to be a homicide detective in Chicago”  
Chuck laughed. “I've missed you so much Casey, we thought you were dead after we didn't hear from you that first year. We have all been a mess, especially Alex, it's been two years Casey.”  
“I didn't have a choice okay, this mission is taking longer than we thought, I had to build up a trust with these people, especially Chandler, It's like becoming John Casey all over again, Alex Coburn's life ended when John Casey's began, then John's ended when Mike's began”  
“How could you just do that though?”  
“It's all I've known Bartowski”  
“What about Verbanski Corp?”  
“Maybe she and Sarah ran off together” He growled.  
“Beckman sent me on this mission and there is absolutely nothing wrong with the computers and no evidence of a hack, there is something else going on, maybe she sent me to bring you home”  
“I don’t think so, we are heading out for a four-month training mission”  
“Casey I don’t want to be on a ship for four months”  
“You need to practice calling me Mike or Slattery”  
“Okay Slattery, we need to call Beckman and figure this out"

There was a knock at the door “Mike is everything okay? I have a message from a General Beckman”  
Casey opened the door to let Tom in who handed Chuck the laptop he was holding.  
“General” Casey couldn't help but smile at the nostalgia.  
“It’s so good to see you, Colonel Casey and Mr. Bartowski, I’m sorry that I lied to you to get you on the ship. And Captian Chandler we have a lot to discuss"  
“Who is Colonel Casey?” Tom looked around  
“John Casey is a CIA agent who we have sent undercover on your ship as Mike Slattery. Chuck is a former CIA agent who we consult with. There were no computer problems, we sent Chuck out to help Dr. Scott with her research, I hope you can still flash Chuck because we need it. Casey I need you to figure out everything about her assistant Quincy as you can”  
“What is going on?”  
“I’m getting there Colonel. There has been an outbreak, last week twenty percent of the population was infected, today we are almost at fifty percent. Dr. Scott has been sent out to find a cure, you will be accompanying her to the Arctic to look for a strain of the virus in a rare bird species, but we think her assistant is working for the Russians sent to destroy all the work she is doing. We need this cure before it wipes out the entire world”  
“You’re lying” Chuck stared at the screen “There is a zombie apocalypse happening?”  
Casey slapped the back of his head “No moron”  
“It’s good to see you two together again. But I’m serious gentleman, we need to keep this quiet and keep communications limited, but we have intel that someone on the ship is sending out the messages and they need to stop. We are almost sure it's Quincy, stop the communication, find the cure and get back to us. Chuck fill Chandler in on the Intersect”  
“Wait, our family back home, how will we know if they are alive? How do we stop from catching it is it air born?”  
“Right now there is no way to tell, they have set up safe places in every major city, It is airborne so as long as you are on the ship away from the population you should be fine, if you come in contact with anyone at all, wear your mask and oxygen tanks”  
“I’ve been on this mission for two years, is that how long this virus has been known about?”  
“No Casey, we knew the Russians were planning something, we just didn’t think it would be this. Good luck gentlemen, I hope to see you soon”

Casey turned to Tom “I’m sorry I lied to you, but I had no choice, I had no idea what my mission was I swear”  
“Your wife, your kids, that summer in the mountains”  
“Cathrine is also an agent, the kids are hers, just not mine. I do have a daughter, she is in her twenties, her name is Alex”  
“That isn’t important right now okay, you two can talk later, I need someone to introduce me to the Doctor and as many of the people on this ship as possible, let's get home to our families"

 

“You and Miller seem to be getting close” Casey said from the bottom bunk  
“You jealous?”  
“No, but Morgan might be”  
Chuck was silent for a minute “John, I’m scared” he was crying.  
“Come down here”  
Chuck climbed down from his bunk, Casey moved the best he could to make room for him in the tiny bunk. They were both laying on their sides facing each other. Casey held him tight holding back his own tears as Chuck buried his face into his chest and cried, his entire body shaking.  
“Ellie, Awesome, Clara, Morgan, Alex” He cried harder “What if they are all gone”  
“I wish I knew what to say to make things better”  
“We have been out here over a month and still haven’t gotten the cure to work, and have gotten no news at all from home”  
“We are doing our best Chuck, that’s all you can do”  
“I haven't been able to flash on anything though”  
“You can only flash on what the CIA knew when they put it in your head, it’s not magic, it’s not just going to tell you all the answers”  
“Alex is pregnant”  
“What?” Casey couldn't hold back his tears anymore.  
“She is just over half-way, It’s a girl. Sorry I didn’t tell you sooner, I was hoping she could tell you herself”  
“I should have came to you instead of Beckman when I left Verbaski, I just wanted to get back into it, get my hands dirty, shoot things. I didn't expect this at all. I didn't know I wouldn't be able to contact any of you and I hope Alex knows I love her and there isn't a day that goes by that I don’t think about her, all of you” They cried themselves to sleep.

 

After that night Casey had not seen Chuck for almost a week, he was getting ready for the day when there was a knock at his door.  
“Hello Rachel”  
“I need you to come down to the lab, Chuck is asking for you”  
“What do you mean?”  
“No one told you? He told me you knew, I’m so sorry Mike, I mean John. He infected himself to test the cure”  
Casey took off running towards the lab, he may have knocked a few people down on the way, he didn’t care, he needed to kill Chuck if he wasn't already dead.  
Casey’s heart sank when he saw Chuck laying in a bed hooked up to an I.V and oxygen  
“John you can’t go in there, he is still contagious”  
“How long?”  
“He infected himself last night, we were about ninety percent sure that we figured it out, he injected himself before I could stop him if the cure doesn't work he probably won't make it to tomorrow”  
“I need to go in there”  
“You have to put a suit on first, you can have zero contact with him or the air inside the tent”

“You’re such a moron Chuck” he grabbed Chuck’s hand.  
“That’s not a nice thing to say to a dying man” Chuck’s voice was weak and muffled by the oxygen mask.  
“I just got you back, I can’t lose you”  
“I’m sorry Casey, I had to. I was so sure it was going to work, I’m so sorry” he body started thrashing around on the bed. Dr. Scott quickly suited up and got to him as the monitor started to beep as Chuck’s heart started to slow down, blood coming from his eyes  
“Chuck come on” Casey winced when the doctor stabbed a needle into Chuck’s chest, he looked at the flat line go across the screen. He pulled Chuck’s lifeless body into his arm, at this point he didn't care if he got infected too. “I love you Bartowski”  
“Did it work?” Miller asked from outside the tent  
“What does it look like Miller?” He laid Chuck down and stood up “No it didn’t fucking work, did you know he was going to do this? You two sure do spend a lot of time together did he tell you his plan?”  
“Dude don’t yell at me, I didn’t do anything”  
“John, look” Rachel pointed to the monitor that was showing a small heartbeat “Chuck? Can you hear me?”  
Casey walked back over to the bed, Chuck groaned “Casey why are you here?”  
“How are you feeling Chuck?” Rachel asked  
“Like crap, did it work?”  
“If it did I’m going to kill you myself, that was really fucking stupid” Casey tried to storm off but he had to go into a decontamination room and take his suit off before he could leave the tented area. 

He stood out on the deck of the ship looking out at the sun setting over the miles of quiet ocean trying to find peace where there was none. Was his daughter still alive, would he make it home to see his granddaughter be born, would Chuck’s family and friends be okay, would the cure work, would the world still fall apart even if they cured the people who are left, was he still in love with Chuck after all this time?  
“Got a lot on your mind Colonel” Tom handed him a cigar.  
“I thought we were saving these?”  
“The cure worked, and it's airborne too, your boy Chuck just has to breath on someone, then they can pass it along and so on, just a simple hug or kiss can save the world or what's left of it. Gator is mapping out our treck back to Norfolk” They lit up their cigars  
“Sorry I’ve lied to you all these years”  
“Just about your name and small little details, but you’re still the same man”  
"Thanks, Chandler"  
“I think you should go talk to him, Dr. Scott told me you were upset”  
“I spend most of my life hiding every emotion except anger, this last month has made me show emotions I didn’t realize I even had any more and seeing someone who I used to, who used to be my best friend laying there dead was hard to take in and I wasn't sure how to deal with it on top of the thought that my daughter may also be dead"  
“Best friend?” a voice came from behind them.  
“I’ll leave you two alone” Tom nodded at him “Thanks Chuck” he patted him on the shoulder when he walked by.  
“We got a message out, not sure who heard it because we haven't gotten anything back so let’s hope there is life left when we get there, they said it will take awhile to get home though”  
Casey didn’t say anything just took a puff of his cigar.  
“I’d like to start off by saying sorry okay I didn’t mean to hurt you, the only thing I was thinking about was finding a way to save people, maybe save our family”  
“Save them just to say hey Chuck is dead but glad your alive to grieve him forever”  
“Well when you put it that way”  
“You should go hang out with your boyfriend or something, I really need to be alone”  
“Excuse me?”  
“Miller, he looked a little sad in there”  
“You’re such an ass, a clearly jealous ass. He is a friend, he is like the only nerd on this ship, of course we are going to be friends, and if I was to date anyone on this ship besides you it would maybe be Burk or Green but him and Kara have that thing they act like isn't a thing but we all know is a thing oh or Wolf, have you see that man fight. But I think sex isnt allowed on the boat technically but I did walk in on Rachel and Tom naked and they tried to come up with a really stupid lie that was actually kinda funny”  
“Did you say besides me?”  
“Did you call be your best friend?” Chuck smirked.  
“I never said that”  
“Just like I’m guessing you didn’t cry and say I love you when I died”  
“That never happened, I actually started throwing a party”  
“Mike Slattery is really bad at lying” Chuck moved closer.  
“I heard the cure can only be passed by kissing”  
“Such a horrible liar” Chuck couldn't help but smile as he pressed their lips together.  
Casey pulled their bodies closer, “Should we take this inside?”  
“What about the no sex rule?”  
“Damn Bartowski, one kiss is all it takes to get in your pants, you are so easy”  
“Shut up, you are the one who invited me inside”  
“Because there are people looking at us”  
“I just saved the world, I think I’m allowed to do whatever I want”  
“And what is it that you want Mr. I saved the world”  
“You” he mumbled into a kiss.

 

When the ship pulled into port there was a huge crowd of people screaming and cheering as they waved American flags in the air.  
All the people aboard the Nathan James were first brought into a building where their surviving friends and family were waiting. Chuck grabbed Casey’s hand and took a deep breath as they walked through the door.  
“Dad” a familiar voice rang through the crowd, Casey looked up just Alex threw herself at him, he wrapped his arms around her and never wanted to let go. “Beckman told me everything, I am so happy that you are alive” she stepped back “We are so happy” she rubbed her stomach.  
"Can I" Casey held his hand up to her belly  
"Of course Grandpa" Her smile was the best thing Casey has seen in a long time.  
She looked at Chuck with tears in her eyes, “Ellie and Clara are here, Clara got knocked down in the chaos and hurt her arm, they are at the med tent, Devon volunteered to help with the sick in Washington D.C. it’s been about a week since we have heard anything but we are hopeful”  
“And Morgan?” Chuck was already crying, Alex shook her head no pulling Chuck into a hug “I’m so sorry Chuck”  
Casey wrapped his arms around both of them.  
“He was so brave, you would have been proud, we were on our way here and we had just hit the border of Kansas when we got ambushed for supplies, he save us”  
Chuck was pulled out of the hug by Ellie “Baby brother it is so good to see your face. When Beckman called and told us what was happening I was so scared for you but I knew you could do it. I’m so proud of you”  
After Chuck and Casey hugged as many people as they could they went back to the house that Ellie, Alex, and Clara had been staying at. Over dinner, they told each other about all the adventures they had had over the last few months and talked about the making a plan to drive up to find Devon and Beckman in Washington D.C.

When Chuck came out of the bathroom Casey was laying on his bed.  
“So Chuck, how does it feel to be a hero?”  
“Rachel deserves all the credit, she is the one who busted her ass, I’m just the guy who was stupid enough to test it”  
“What are your plans now? After we find Devon?”  
“I have no idea, I guess head back to Burbank and see if I can get Carmichael Industries back up and running” he started crying again, he didn’t think it was possible to any more tears left after how much he just cried in the shower. “It just hit me again that Morgan is gone, I don’t think I can run C.I. without him”  
Casey pulled him down into the bed with him wrapping his arms around him as tight as he could. “I’m so sorry Chuck” he kissed the top of his head “I know I’m not a nerd, but if you want I will help you”  
“I thought Mike Slattery would want to go back to his wife and kids”  
“Oh shit you’re right, let me leave my real daughter, granddaughter and boyfriend to go live with my fake family”  
“I’d understand if you didn’t want to continue this now that we are home”  
“Did you fall and hit your head while you were in there? Or do you want me to call Wolf and see if he is still single?"  
“Shut up, I just thought since we didn’t tell Ellie and Alex about us that maybe it was over”  
“You think too much, there was a lot to talk about and I didn’t think our sex life was an important part of the story”  
“What about the part where you said you loved me”  
“I said no such thing” Casey smirked.  
“Wasn’t lying what got you into this in the first place?”

 

They found Devon at a hospital in D.C. where they all decided to stay, it took a few months before they were able to get a plane back to Burbank to pack up anything left in their apartments. It wasn't long after that when Alex gave birth to her daughter who she named Morgan. It was six months after that when Ellie came home and told Chuck about a one-year-old little boy who lost both his parents during the outbreak and was found living alone in an apartment and was finally being let out of the hospital. Chuck and Casey didn't even need to talk about, they brought him home the next day and since he couldn't talk when he parents passed he didn't have a name, they decided on Nathan, after the ship that brought them back together to save the world.  
Eventually, they got married, Alex stood in for Morgan as Chuck's best "man" while Tom stood next to Casey. And no matter how much Chuck begged Casey did not wear his dress whites since technically he wasn't in the Navy anymore.  
Casey and Chuck reopened Carmichael Industries with the help of General Beckman, with the promise of no more missions on ships of any kind.  
It took a long time, but eventually, the world got back to its normal routine.


End file.
